User: sam237337

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sam23733750
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Posts by sam237337

<prev • 14 results • page 1 of 2 • next >
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Most efficient way to obtain L1000 small molecule perturbagen drug names?
... I'm seeking to obtain the complete list of all small-molecule perturbagens used in the LINCS L1000 drug perturbation dataset. I have reviewed available resources including the following: LINCS Data Portal: http://lincsportal.ccs.miami.edu/dcic-portal/ Connectivity Map website: https://clue.io/ Th ...
data extraction l1000 written 9 weeks ago by sam23733750
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Comment: C: Most efficient strategy to convert from Ensembl protein IDs (ENSP) to Entrez Gen
... Thanks for your clarification, Emily; I will plan to try using BioMart again, beyond my initial experience with that platform that hadn't been successful. I think that it is frowned upon in forum etiquette to reply to each individual response with a thank-you message, so I will let this response se ...
written 8 months ago by sam23733750
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Most efficient strategy to convert from Ensembl protein IDs (ENSP) to Entrez Gene Symbols?
... I have a list of Ensembl protein IDs (ENSP) that I need to convert to Entrez-formatted gene symbols. So far, I haven't identified a straightforward method to convert between these two formats, as I'm not seeing a platform that will permit this. This is my current tentative strategy: Step 1: Convert ...
conversion written 8 months ago by sam23733750 • updated 8 months ago by vkkodali1.1k
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Comment: C: Availability of DrugMatrix database?
... Update: An alternative platform that provides the set of DrugMatrix samples is [GEO][1], and the processed signatures can be accessed on the [CREEDS platform][2]. [1]: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_geo_query_acc.cgi-3Facc-3DGSE59927&d=DwMFaQ&c= ...
written 15 months ago by sam23733750
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Availability of DrugMatrix database?
... I have been attempting to access the [DrugMatrix toxicogenomics database][1] for the past few weeks, but continue to see a ["Website Offline" message][2] at this site. I had emailed the provided contact a few weeks ago to inquire about its availability, but I haven't received a response. Does anyone ...
database drug written 15 months ago by sam23733750
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Comment: C: Availability of Broad Institute BRD perturbagen identifier mappings?
... Update: This solution doesn't directly address the question I originally posed, but I did find that the [LINCS Small Molecules Catalog][1] site contains the mappings between LINCS LSM ID values (which are also included in my dataset) and drug names, so that I ultimately didn't need the mappings for ...
written 15 months ago by sam23733750
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Availability of Broad Institute BRD perturbagen identifier mappings?
... I have a dataset that includes identifiers from the Broad Institute of the format BRD-{9-valued alphanumeric string}, where each ID specifies a perturbagen. I'm trying to locate a master list of the definitions/names of these BRD IDs, specifying how they map to other platforms such as PubChem and Ch ...
mappings identifiers written 15 months ago by sam23733750
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Comment: C: Comprehensive & integrated drug/target database?
... Thanks for your helpful suggestions, Denise! I will definitely explore them. ...
written 15 months ago by sam23733750
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Comment: C: Best way to deal with numerous synonyms when converting between drug identifiers
... Many thanks for the info you provided, Natasha! I will review it in detail, as it seems like it will be very helpful. ...
written 16 months ago by sam23733750
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Comprehensive & integrated drug/target database?
... The [Drug2Gene resource][1] integrates 19 different drug-target databases, and is distinguished by its standardization and unification across those different platforms (including ChEMBL, DrugBank, Uniprot, HGNC and ChEBI). However, when attempting to access this resource (http://www.drug2gene.com) f ...
database drug target written 16 months ago by sam23733750 • updated 16 months ago by Denise - Open Targets5.0k

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